How DNA Sequencing Has Changed the Way Listeria Outbreaks Are Tracked

Health officials are now able to use whole genome sequencing techniques to track the spread of dangerous Listeria outbreaks.

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By the time you hear about a listeria outbreak on the news, public health officials have already been hard at work tracking that outbreak back to its source. The faster that source is identified, the sooner health authorities can contain it — and the fewer people will get sick.

Recent Food-Borne Illness Outbreaks

Health officials also use a form of analysis called pulsed-field gel electrophoresis, or PFGE, to identify related strains of Listeria. They look at DNA fragments of suspected contaminated foods or molecules after sending an electrical current through it, and then compare it with molecules known to be Listeria monocytogenes. (2)

But this form of analysis isn’t always accurate. (3) “With PFGE, unrelated Listeria germs can sometimes look similar, and closely related ones can look different,” states a fact sheet from the Centers for Disease Control and Prevention (CDC). (3)

While patient interviews and PFGE are still an important part of outbreak management, health officials have a powerful new tool in their arsenal: whole genome sequencing. (4)

Health Officials Have Been Using Whole Genome Sequencing to Track Listeria Outbreaks Since 2013

“There are many, many different genetic variants of Listeria,” explains Janet Donaldson, PhD, a professor of cell and molecular biology at the University of Southern Mississippi, in Hattiesburg. “Some distinct variants of Listeria, called strains, harbor genes that can promote growth in the GI tract, while other strains do not.”

Each of these strains has a subtly different genetic blueprint. Since 2013, public health officials have been able to use whole genome sequencing to examine that blueprint in order to precisely identify the exact strain of Listeria monocytogenes that is making a person sick. (3)

Why is this helpful? Not all listeria-related outbreaks are linked to a specific food product. Some may start on a piece of food-processing equipment that handles multiple foods. If those contaminated foods are then included in different food products and sent all over the country, it can be very difficult for experts to track those seemingly unconnected listeriosis cases back to their shared source.

“If listeria illnesses occur far apart, current methods cause health officials to lose time figuring out which illnesses are part of an outbreak,” the CDC reports. (3)

Whole genome sequencing allows officials to connect dots in ways they couldn’t before. If the same exact strain of Listeria turns up in people with listeriosis in Ohio and also in Nevada — people who haven’t eaten the same foods — officials know to dig deeper. In at least one case, experts have used whole genome sequencing to uncover a furtive listeria outbreak that persisted for five years and would likely not have been identifiable without whole genome sequencing. (3)

Thanks to the sequencing technique, “more outbreaks have been identified with fewer cases and in foods not previously a focus of investigation,” reported the authors of a 2017 review study published in Food Control. (5) The CDC’s whole genome sequencing program has been so successful that the agency has expanded its program to include other illness-causing bacteria — including Campylobacter and E. coli. (3)

Health experts are using genome sequencing for more than just outbreak identification. A map of a listeria bacterium’s DNA can also help them develop new and more effective therapies. “What I am working on in my lab is how listeria responds to the different environments in the GI tract to survive,” Dr. Donaldson says.

Most bacteria cannot withstand the acidic environment of the stomach and upper intestine. But Listeria monocytogenes is different. Not only can it survive the perils of the upper GI tract, but it has the ability to invade its host’s cells and multiply, despite the absence of nutrients found inside those cells. From there, listeria can work its way into a patient’s bloodstream, where it causes invasive and sometimes deadly infections. (6)

Donaldson says her research in part investigates how illness-causing listeria bacteria “sense” oxygen variations in the GI tract, and how this may help them survive (and cause problems for its hosts).

It’s difficult to defeat a foe if you don’t understand how it operates. So understanding all these processes behind listeria bacteria's success is important.

Donaldson’s work and the research of others using whole genome sequencing should help inform the development of new and better treatments. “If we can figure out how listeria respond to the GI tract, we can design therapeutics targeting these mechanisms to block the ability of listeria to get into the blood,” she says.

Whole Genome Sequencing May Some Day Help Stop Listeria Outbreaks Before They Start

Finally, whole genome sequencing could also help officials figure out how Listeria monocytogenes is able to survive and flourish in conditions that prevent other types of bacteria from spreading — which could help reveal strategies to prevent listeria outbreaks in the first place.

Even when a food is contaminated with listeria bacteria, its levels of harmful bacteria are often not high enough to cause sickness in humans — at least not at first. But Listeria monocytogenes has the ability to stay alive and spread even at refrigeration temperatures. So as a contaminated food sits around in a refrigerator or freezer, its listeria bacteria continue to reproduce until their levels are great enough to cause infection. (7)

Using whole genome sequencing, experts can better understand how listeria is able to survive and spread in refrigerated conditions. They can also gain insights into the ways listeria contaminates food-processing equipment — even when that equipment is thoroughly cleaned and treated with disinfectant. With these insights, they may be able to prevent food contamination, and so prevent people from ever being exposed to harmful levels of the bacteria.

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